How do you account for whether the kid came out of HS or college as a jr or sr(different development/age schedules), things like Tommy John that delay a prospect's development but not a long-term indicator of failure anymore?

Well again Tommy John falls into the large problem that we're only looking at one season. PECOTA which won't be around for months, uses three seasons of data so for most prospects, a season where a player is missing significant time tends to lead to comps of other players with injuries that kept them out. But surgery is a good place where you have to use your own analysis and insight and proves why statistical models are never perfect, they're simply an aide.

As far as whether a player came out of HS, JUCO, College, etc. the belief is that aside from age, which is taken into account, those factors matter very little. Obviously a player that doesn't leave college until he's a high school senior will never be able to reach high A at 19 as Sweeney has but theoretically if he's ability's the same then when he's 22 and making his debut he'll be at a high level or will advance extremely quickly. A college player can't ever reach the majors at 19 or 20 but those events are extremely rare. Players like Prior, Alex Fernandez, or Ryan Wagner have made it in little or not time.